Week 7: Continuous character models
#install.packages("yearn")
library(ape)
library(geiger)
library(OUwie)
## Loading required package: nloptr
## Loading required package: lattice
library(phytools)
#library(devtools)
#devtools::install_github("phylotastic/rphylotastic")
library(rphylotastic)
## This data come from Brandley et al. (2008)
sqData<-read.csv("brandley_table.csv")
sqTree<-read.nexus ("squamate.tre.txt")
plotTree(sqTree,ftype="i",lwd=1)

speciesNames<-sqData[,1]
speciesNames
species<-sub(" ","_",speciesNames)
sqData[,1]<-species
head(sqData)
CleanData <- function(phy, data) {
speciesNames<-unlist(data[,1], use.names = FALSE)
cleaned.names.data<-taxa_resolve_names_with_gnr(speciesNames)
cleaned.names.phy<-taxa_resolve_names_with_gnr(phy$tip.label)
phy.cleaned.names<-phy
phy.cleaned.names$tip.label <- cleaned.names.phy
data.vector<-data[,2]
names(data.vector)<-cleaned.names.data
cleaned.data<-treedata(phy.cleaned.names,data.vector, sort=TRUE, warnings=TRUE)
return(cleaned.data)
}
cleaned.data<-CleanData(sqTree,sqData)
## Warning in treedata(phy.cleaned.names, data.vector, sort = TRUE, warnings = TRUE): The following tips were not found in 'phy' and were dropped from 'data':
## Gonatodes albogularis
## Lepidophyma flavimaculatum
## Trachyboa boulengeri
VisualizeData <- function(phy, data) {
diagnostic<-contMap(phy, data, res=100, fsize=NULL, ftype=NULL, lwd=4, legend=NULL,
lims=NULL, outline=TRUE, sig=3, type="phylogram", direction="rightwards",
plot=FALSE)
plot(diagnostic)
}
VisualizeData(cleaned.data$phy,cleaned.data$data[,1])

## Brownian motion is a stochastic model in which changes from one time to the next are random draws from a normal distribution with mean 0.0 and variance σ2 × Δt. In other words, the expected variance under Brownian motion increases linearly through time with instantaneous rate σ2.
BM2<-fitContinuous(cleaned.data$phy,cleaned.data$data[,1],model="BM")
BM2
## GEIGER-fitted comparative model of continuous data
## fitted 'BM' model parameters:
## sigsq = 138.341054
## z0 = 169.171661
##
## model summary:
## log-likelihood = -1502.985290
## AIC = 3009.970579
## AICc = 3010.017638
## free parameters = 2
##
## Convergence diagnostics:
## optimization iterations = 100
## failed iterations = 0
## frequency of best fit = 1.00
##
## object summary:
## 'lik' -- likelihood function
## 'bnd' -- bounds for likelihood search
## 'res' -- optimization iteration summary
## 'opt' -- maximum likelihood parameter estimates
#Here we see that the rate of evolution is 138.341054 in 169.171661 unit of time.
OU1 <- fitContinuous(cleaned.data$phy, cleaned.data$data, model="OU")
## Warning in fitContinuous(cleaned.data$phy, cleaned.data$data, model = "OU"):
## Non-ultrametric tree with OU model, using VCV method.
## Warning in cache$dat - mu: Recycling array of length 1 in vector-array arithmetic is deprecated.
## Use c() or as.vector() instead.
## Warning in cache$dat - mu: Recycling array of length 1 in vector-array arithmetic is deprecated.
## Use c() or as.vector() instead.
ou.tree <- rescale(cleaned.data$phy, model="OU", 0.005)
par(mfcol=(c(1,2)))
plot(cleaned.data$phy, show.tip.label=FALSE)
plot(ou.tree)

##These trees are slighly differents. The second tree vary according to the value of a. As a, the parameter used for transformation increase, the time for diversifation decrease
AIC.BM2 <- BM2$opt$aicc
AIC.OU1 <- OU1$opt$aicc
AIC.BM2
## [1] 3010.018
AIC.OU1
## [1] 3012.065
delta_aic<-function(x) x-x[which(x==min(x))]
delta_aic(c(AIC.BM2, AIC.OU1))
## [1] 0.000000 2.047407
## it seems like the he Brownian motion model (Felsenstein 1973) looks better because it has the smallest AIC
#one.discrete.char <-limbs
reconstruction.info <- ace(cleaned.discrete$data,cleaned.discrete$phy, type="discrete", method="ML", CI=TRUE)
best.states <- colnames(reconstruction.info$lik.anc)[apply(reconstruction.info$lik.anc, 1, which.max)]
class(best.states)
## [1] "character"
library(OUwie)
## The function Ouwie uses a data frame with three columns. First columns with species names. The second column is the selective regime and the third one is the continuous traits
newdat <-data.frame(names=rownames(cleaned.data$data))
#str(newdat)
#newdat[,1]
#newdat[,2]
cleaned.data$phy$node.label<-best.states
newdat <-data.frame(names=rownames(cleaned.data$data),regime=cleaned.discrete$data[[1]], trait=cleaned.data$data[,1])
nodeBased.OUMV <- OUwie(cleaned.data$phy, newdat,model="OUMV", simmap.tree=FALSE, diagn=FALSE)
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
print(nodeBased.OUMV)
##
## Fit
## lnL AIC AICc BIC model ntax
## -1470.432 2950.863 2951.101 2968.628 OUMV 258
##
##
## Rates
## 1 2
## alpha 2.345336e-09 2.345336e-09
## sigma.sq 2.922578e+02 4.516810e+00
##
## Optima
## 1 2
## estimate 469.6925 88.61548
## se 135.7585 18.65365
##
##
## Half life (another way of reporting alpha)
## 1 2
## 295542742 295542742
##
## Arrived at a reliable solution
library(OUwie)
models <- c("BM1","BMS","OU1","OUM","OUMV","OUMA","OUMVA")
runmod<-function(phy, data, models){
mod<-OUwie(phy, data, models, simmap.tree = F, diagn = F)
}
## running lapply
results<- lapply(models, runmod, phy = cleaned.data$phy, data = newdat)
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
## Warning: By setting root.station=TRUE, you have specified the group means model
## of Thomas et al. 2006
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
results$AICc
## NULL
AICc.values<-sapply(results, "[[", "AICc")
names(AICc.values)<-models
AICc.values<-AICc.values-min(AICc.values)
best<-results[[which.min(AICc.values)]]
?OUwie.fixed
# Nornally alpha vary from exp(-500) to exp(1). But let take these values
alpha.values<-seq(from=1.637367e-06 , to= 0.2664882 , length.out=50)
library(OUwie)
likelihood.values <- rep(NA, length(alpha.values))
best$solution
## 1 2
## alpha 1.637367e-06 0.2664882
## sigma.sq 2.150683e+00 2.1506830
for (iteration in sequence(length(alpha.values))) {
likelihood.values[iteration] <- OUwie.fixed(cleaned.data$phy, newdat, model="OUMV", alpha=rep(alpha.values[iteration],2), sigma.sq=best$solution[2,], theta=best$theta[,1])$loglik
}
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 1.637367e-06 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.005440139 0.005440139 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.01087864 0.01087864 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.01631714 0.01631714 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.02175564 0.02175564 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.02719414 0.02719414 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.03263265 0.03263265 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.03807115 0.03807115 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.04350965 0.04350965 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.04894815 0.04894815 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.05438665 0.05438665 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.05982515 0.05982515 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.06526365 0.06526365 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.07070215 0.07070215 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.07614066 0.07614066 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.08157916 0.08157916 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.08701766 0.08701766 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.09245616 0.09245616 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.09789466 0.09789466 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.1033332 0.1033332 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.1087717 0.1087717 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.1142102 0.1142102 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.1196487 0.1196487 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.1250872 0.1250872 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.1305257 0.1305257 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.1359642 0.1359642 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.1414027 0.1414027 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.1468412 0.1468412 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.1522797 0.1522797 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.1577182 0.1577182 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.1631567 0.1631567 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.1685952 0.1685952 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.1740337 0.1740337 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.1794722 0.1794722 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.1849107 0.1849107 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.1903492 0.1903492 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.1957877 0.1957877 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.2012262 0.2012262 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.2066647 0.2066647 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.2121032 0.2121032 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.2175417 0.2175417 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.2229802 0.2229802 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.2284187 0.2284187 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.2338572 0.2338572 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.2392957 0.2392957 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.2447342 0.2447342 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.2501727 0.2501727 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.2556112 0.2556112 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.2610497 0.2610497 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 0.2664882 0.2664882 2.150683 2.150683 1.677575e-18 159.0305
plot(x=alpha.values , y= likelihood.values, xlab=" alpha", ylab="maximum log-likelihood", type="l", bty="n")
points(x=best$solution[1,1], y=best$loglik, pch=16, col="red")
text(x=best$solution[1,1], y=best$loglik, "unconstrained best", pos=4, col="red")

require("akima")
## Loading required package: akima
nreps<-400
theta1.points<-c(best$theta[1,1], rnorm(nreps-1, best$theta[1,1], 5*best$theta[1,2])) #center on optimal value, have extra variance
theta2.points<-c(best$theta[2,1], rnorm(nreps-1, best$theta[2,1], 5*best$theta[2,2])) #center on optimal value, have extra variance
likelihood.values<-rep(NA,nreps)
for (iteration in sequence(nreps)) {
likelihood.values[iteration] <- OUwie.fixed(cleaned.data$phy, newdat, model="OUMV", alpha=best$solution[1,], sigma.sq=best$solution[2,], theta=c(theta1.points[iteration], theta2.points[iteration]))$loglik
}
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 159.0305
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1256958
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -5108927
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 280797.4
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1742580
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1774691
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1114493
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1081749
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 4861876
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 9517511
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1837012
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3447071
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -7743580
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2311845
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1699906
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2468626
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3003052
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1929928
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 6681833
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -632171.9
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1172987
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2741382
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 5016135
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2326475
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1044548
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -7058719
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1244367
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 6046958
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2020140
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 5201214
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -5023770
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -78784.25
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -43164.11
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1995959
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -440708.3
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1006343
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -587679.6
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -214644.3
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -28124.72
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -4033735
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3355173
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3990348
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3674228
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3790716
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -901767.1
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -921405.5
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2123703
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -5374991
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2226227
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3386057
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1872787
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3551091
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1254241
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2040624
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3611460
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -6385081
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2057123
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1316010
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -295584.8
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2338872
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3006416
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2567166
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1302752
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2406016
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1671299
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -72597.71
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2562961
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3043107
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 5093718
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1022334
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3716601
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1396627
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 976005
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -96546.48
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1406843
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -5329075
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 416686.4
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -102773.3
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3115330
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1068125
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1485029
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3722890
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 847575.4
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -644073.2
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2938303
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -228084
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1312436
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1977171
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2920186
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1808449
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -45893.05
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2804217
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -274156.9
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -317641
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3553812
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 6124487
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2506002
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2893439
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2145328
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2241082
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1795065
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3378528
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 981803.6
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -485273.3
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -6671355
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -768733
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3174114
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -346911.7
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1425594
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 6199020
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 5788667
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3321590
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1401294
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 107591.8
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1741277
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -4226271
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 394183.7
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3302468
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -140401.9
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1208361
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2790002
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2920632
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -837206.9
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -6778217
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2578024
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2468515
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2588458
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2008229
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -4345764
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3081518
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1113222
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1092131
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -355978.1
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2616439
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -344269.6
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -186141.1
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2914360
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3535281
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1369313
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 522066.8
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1905726
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2744309
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 4019549
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3784742
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 462888.5
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1719577
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 338646.5
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3645409
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3015618
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1528465
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1707182
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1914885
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -4533111
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2603059
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3031292
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -4232358
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 345835.5
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1577886
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2007531
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 7235881
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -264870.6
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 5641723
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 5714594
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2853574
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1410716
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -5843308
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 4810239
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1602910
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 849110.1
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1333600
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3009683
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 343426.3
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1054663
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 612998.3
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -6661169
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1178274
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -264364.5
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -4281310
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2252851
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1161303
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 189143.8
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1246893
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2079298
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2883289
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1446956
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1271910
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1500603
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3230099
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 208011.4
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -596918.9
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -4546760
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -974234.8
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1070153
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 6764738
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1954006
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -94534.67
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3980758
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -4859320
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -810287.7
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -5564906
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1734752
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1221285
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2990382
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 4149985
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3279638
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2472143
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -379187.4
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3026035
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1939205
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3498877
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -5535561
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2997329
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2236505
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 40908.34
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1765265
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 820362.2
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3504296
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2168558
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2659821
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -5058869
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2866258
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 524523
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -974200
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 214402.9
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1517492
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -177400.9
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -4689175
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 371448.1
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2567495
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1638529
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1563458
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2791330
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2557416
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -712691.7
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2409769
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 856191.2
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2381688
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2916387
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1525092
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -4597151
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 4333121
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -718225.4
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1944294
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 4285002
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 442352.8
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3573586
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1945638
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1581835
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -39012.81
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 898571.9
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1330224
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3495947
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1774798
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2604796
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2074008
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 600310.6
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 952935.5
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 4177272
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1628107
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 711883.4
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2198573
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3082067
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3006118
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -32610.93
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1159194
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 398839.5
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1049997
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1512477
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2143218
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1353167
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2310284
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2653016
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2699224
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1528723
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1179652
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 6825488
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1951266
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 5542194
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3073573
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1379910
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2201715
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -4741683
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3629994
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2731008
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 128721.9
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 5876244
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -385899.6
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -273110.5
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2551368
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3979835
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 377963.2
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 631254.8
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1713103
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -377980.2
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1737135
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 4791409
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2417684
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -269510.7
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3866439
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2524496
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 847113.7
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -5113443
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 738041.6
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 6279009
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -5306236
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 193849.7
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -4319506
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3795402
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1246299
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2650034
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 947299.6
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2894896
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -4962997
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -44766.25
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3850120
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -683400.1
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 5860049
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 676304.8
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 67650.96
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1027356
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2631264
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -105655.2
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1300968
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 4624073
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 8225380
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2715684
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2389402
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2991660
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2077857
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3683973
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1230331
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3614534
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 4593838
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -172402.1
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -807836.6
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 5499924
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 341406.1
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3380500
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3918513
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2827225
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1641988
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -498529.9
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3010393
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1214654
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -383216.2
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3702799
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3327023
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 992432.7
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2021175
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 5950725
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3749353
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1335822
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -5690074
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1237398
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 385722
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1264650
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2166391
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1899854
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3280471
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 988426.2
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1623257
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 230623.5
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -739987.6
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1017374
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3412157
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -791644.1
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1350730
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 4067394
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -881886.8
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 6648255
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 388369.4
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 5525223
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1041336
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2650118
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 445737.1
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3520692
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 7212027
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 807546.9
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 5650307
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -927675
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1970863
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 983662.5
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -340115.3
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 3211935
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -2349708
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 195905.4
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -344951.7
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 4711363
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -1514516
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -4834808
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1083226
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -6082596
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 6057833
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -748843.9
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 703619.9
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -3284674
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 -442116.8
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 301761.3
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 1120827
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Calculating likelihood using fixed parameter values: 1.637367e-06 0.2664882 2.150683 2.150683 1.677575e-18 2057784
likelihood.differences<-(-(likelihood.values-max(likelihood.values)))
library(akima)
interpolated.points<-interp(x=theta1.points, y=theta2.points, z= likelihood.differences, linear=FALSE, extrap=TRUE, xo=seq(min(theta1.points), max(theta1.points), length = 400), yo=seq(min(theta2.points), max(theta2.points), length = 400))
contour(interpolated.points, xlim=range(c(theta1.points, theta2.points)),ylim=range(c(theta1.points, theta2.points)), xlab="Theta 1", ylab="Theta 2", levels=c(2,5,10),add=FALSE,lwd=1, bty="n", asp=1)
points(x=best$theta[1,1], y=best$theta[2,1], col="red", pch=16)
points(x=newdat$X[which(newdat$Reg==1)],y=rep(min(c(theta1.points, theta2.points)), length(which(trait$Reg==1))), pch=18, col=rgb(0,0,0,.3)) #the tip values in regime 1, plotted along x axis
points(y=newdat$X[which(newdat$Reg==2)],x=rep(min(c(theta1.points, theta2.points)), length(which(trait$Reg==2))), pch=18, col=rgb(0,0,0,.3)) #the tip values in regime 2, plotted along y axis
library(phytools)
trait.ordered<-data.frame(cleaned.discrete$data[,1], cleaned.discrete$data[,1])
z<-trait.ordered[,1]
names(z)<-rownames(trait.ordered)
tree.mapped<-make.simmap(cleaned.discrete$phy,z,model="ER",nsim=1)
## make.simmap is sampling character histories conditioned on the transition matrix
##
## Q =
## 1 2
## 1 -0.001864317 0.001864317
## 2 0.001864317 -0.001864317
## (estimated using likelihood);
## and (mean) root node prior probabilities
## pi =
## 1 2
## 0.5 0.5
## Done.
leg<-c("black","red")
names(leg)<-c(1,2)
plotSimmap(tree.mapped,leg,pts=FALSE,ftype="off", lwd=1)

simmapBased<-OUwie(tree.mapped,newdat,model="OUMV", simmap.tree=TRUE, diagn=FALSE)
## Warning: Some dates are negative? rootAge may be incorrectly defined or you are using a time-scaling method that warps the tree, like aba or zbla.
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
print(simmapBased)
##
## Fit
## lnL AIC AICc BIC model ntax
## -1472.461 2954.922 2955.16 2972.687 OUMV 258
##
##
## Rates
## 1 2
## alpha 1.276258e-03 0.001276258
## sigma.sq 4.380271e+02 84.996120708
##
## Optima
## 1 2
## estimate 264.3087 132.33690
## se 149.1609 53.14754
##
##
## Half life (another way of reporting alpha)
## 1 2
## 543.1091 543.1091
##
## Arrived at a reliable solution
print(best)
##
## Fit
## lnL AIC AICc BIC model ntax
## 1523.125 -3036.25 -3036.012 -3018.485 OUMA 258
##
##
## Rates
## 1 2
## alpha 1.637367e-06 0.2664882
## sigma.sq 2.150683e+00 2.1506830
##
## Optima
## 1 2
## estimate 1.677575e-18 159.0305
## se 0.000000e+00 561805.9172
##
##
## Half life (another way of reporting alpha)
## 1 2
## 4.233304e+05 2.601043e+00
##
## Arrived at a reliable solution